Multi-dimensional annotation of porcine variants using genomic and epigenomic features in pigs.

Journal: BMC biology
Published Date:

Abstract

BACKGROUND: Investigating the functional impact of genomic variants is essential to uncover the molecular mechanisms behind complex traits. This study compiled a comprehensive dataset of 1,817 whole-genome sequences from diverse pig breeds and populations, capturing the global pig genetic diversity.

Authors

  • Hongwei Yin
    School of Information Engineering, Huzhou University, Huzhou 313000, China.
  • Liu Yang
    Department of Ultrasound, Hunan Children's Hospital, Changsha, China.
  • Qianyi Zhao
    Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, CAAS, Building A, Room 311, Buxin Road, Dapeng, Shenzhen, 518124, China.
  • Wenye Yao
    Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, CAAS, Building A, Room 311, Buxin Road, Dapeng, Shenzhen, 518124, China.
  • Jinyan Teng
    National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China.
  • Yahui Gao
    State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University (SCAU), Guangzhou, China.
  • Zhiting Xu
    National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China.
  • Qing Lin
    National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China.
  • Shuqi Diao
    National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China.
  • Xiaohong Liu
    Department of Biopharmaceutics, School of Pharmacy, Shenyang Pharmaceutical University, Wenhua Road, Shenyang 110016, China. Electronic address: lvj221@163.com.
  • Fuping Zhao
    State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road, Beijing, 100193, China.
  • Zhongyin Zhou
    Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China.
  • Qishan Wang
    Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.
  • Jiaqi Li
    Department of Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, People's Republic of China.
  • Zhe Zhang
    Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China.
  • Huaijun Zhou
    Department of Animal Science, University of California, Davis, CA, 95616, USA.
  • Martien A M Groenen
    Animal Breeding and Genomics, Wageningen University and Research, Wageningen, 6708 PB, The Netherlands.
  • Ole Madsen
    Department for Materials and Production, Aalborg University, 9220 Aalborg, Denmark.
  • Lijing Bai
    Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, CAAS, Building A, Room 311, Buxin Road, Dapeng, Shenzhen, 518124, China. bailijing@caas.cn.
  • Dailu Guan
    Department of Animal Science, University of California, Davis, CA, 95616, USA. dguan@ucdavis.edu.
  • Lingzhao Fang
    Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural UniversityBeijing, China; Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus UniversityTjele, Denmark.
  • Kui Li
    Department of Radiology, Women'S Hospital, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, Zhejiang, 310006, China.

Keywords

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